[gmx-users] Justin tutorial - V-rescale + Parinello-Rahman

[Justin Lemkul]

On 4/9/14, 8:18 AM, Steven Neumann wrote:
> Dear Gmx Users, Dear Justin
>
> I have noticed that in in our tutorial(s) in thew mdp option you suggesting
> V-rescale thermostat and the Parinello-Rahman barostat. Is there any
> particular reason for this choice? Would you please provide any reference
> that is combinantion works well in comparison to others or its just the
> example?
>

The original references for each of the algorithms prove that they adequately 
sample the desired ensembles.  For the purposes of tutorials, these algorithms 
are robust, and I avoid Berendsen because I experience has shown me that people 
simply assume that whatever is in the tutorial is "correct" so I at least 
attempt to avoid leading people into making mistakes.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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